In vitro characterization of a miR-122-sensitive double-helical switch element in the 5′ region of hepatitis C virus RNA

Nucleic Acids Research

Volumn 37, Issue 16, 2009, Pages 5498-5510

  Díaz toledano, Rosa ^a,b   Ariza mateos, Ascensión ^a   Birk, Alex ^c   Martínez Garcí, Belén ^a   Gómez, Jordi ^a,b  

^a INSTITUTO DE PARASITOLOGÍA Y BIOMEDICINA LÓPEZ NEYRA   (Spain)

^b INSTITUTO DE SALUD CARLOS III   (Spain)

^c BARUCH S BLUMBERG INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA; MICRORNA; RIBONUCLEASE III; VIRUS RNA; RIBONUCLEASE; RIBONUCLEASE T1; RIBONUCLEASE V(1);

5' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; ESCHERICHIA COLI; GENE SWITCHING; HEPATITIS C VIRUS; IN VITRO STUDY; INTERNAL RIBOSOME ENTRY SITE; NONHUMAN; PRIORITY JOURNAL; RNA ANALYSIS; RNA CONFORMATION; RNA TRANSLATION; STRUCTURE ANALYSIS; CHEMISTRY; CONFORMATION; ENZYMOLOGY; GENETICS; KINETICS; METABOLISM; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; POLYACRYLAMIDE GEL ELECTROPHORESIS; SEQUENCE ANALYSIS;

ESCHERICHIA COLI; HEPATITIS C VIRUS;

5' UNTRANSLATED REGIONS; BASE SEQUENCE; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ENDORIBONUCLEASES; ESCHERICHIA COLI; HEPACIVIRUS; KINETICS; MICRORNAS; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; RIBONUCLEASE III; RIBONUCLEASE T1; RNA, VIRAL; SEQUENCE ANALYSIS, RNA;

EID: 70449729916     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp553     Document Type: Article

References (21)

1. Reynolds,J.E., Kaminski,A., Carroll,A.R., Clarke,B.E., Rowlands,D.J. and Jackson,R.J. (1996) Internal initiation of translation of hepatitis C virus RNA: the ribosome entry site is at the authentic initiation codon. RNA, 2, 867-878.
2. Jopling,C.L., Yi,M., Lancaster,A.M., Lemon,S.M. and Sarnow,P. (2005) Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA. Science, 309, 1577-1581.
3. McMullan,L.K., Grakoui,A., Evans,M.J., Mihalik,K., Puig,M., Branch,A.D., Feinstone,S.M. and Rice,C.M. (2007) Evidence for a functional RNA element in the hepatitis C virus core gene. Proc. Natl Acad. Sci. USA, 104, 2879-2884.
4. Vassilaki,N., Friebe,P., Meuleman,P., Kallis,S., Kaul,A., Paranhos-Baccala,G., Leroux-Roels,G., Mavromara,P. and Bartenschlager,R. (2008) Role of the hepatitis C virus core+1 open reading frame and core cis-acting RNA elements in viral RNA translation and replication. J. Virol., 82, 11503-11515.
5. Kim,Y.K., Lee,S.H., Kim,C.S., Seol,S.K. and Jang,S.K. (2003) Long-range RNA-RNA interaction between the 5' nontranslated region and the core-coding sequences of hepatitis C virus modulates the IRES-dependent translation. RNA, 9, 599-606.
6. Honda,M., Rijnbrand,R., Abell,G., Kim,D. and Lemon,S.M. (1999) Natural variation in translational activities of the 5' nontranslated RNAs of hepatitis C virus genotypes 1a and 1b: evidence for a long-range RNA-RNA interaction outside of the internal ribosomal entry site. J. Virol., 73, 4941-4951.
7. Beguiristain,N., Robertson,H.D. and Gomez,J. (2005) RNase III cleavage demonstrates a long range RNA: RNA duplex element lanking the hepatitis C virus internal ribosome entry site. Nucleic Acids Res., 33, 5250-5261.
8. Tuplin,A., Evans,D.J. and Simmonds,P. (2004) Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods. J. Gen. Virol., 85, 3037-3047.
9. Milligan,J.F. and Uhlenbeck,O.C. (1989) Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol., 180, 51-62.
10. Franklin,R.M. (1966) Purification and properties of the replicative intermediate of the RNA bacteriophage R17. Proc. Natl Acad. Sci. USA, 55, 1504-1511.
11. Robertson,H.D. (1967) A Nuclease Specific for Double-Stranded RNA. Virology, 12, 718-719.
12. Nicholson,A.W. (1999) Function, mechanism and regulation of bacterial ribonucleases. FEMS Microbiol. Rev., 23, 371-390.
13. Nadal,A., Martell,M., Lytle,J.R., Lyons,A.J., Robertson,H.D., Cabot,B., Esteban,J.I., Esteban,R., Guardia,J. and Gomez,J. (2002) Specific cleavage of hepatitis C virus RNA genome by human RNase P. J. Biol. Chem., 277, 30606-30613.
14. Dunn,J.J. (1976) RNase III cleavage of single-stranded RNA. Effect of ionic strength on the fideltiy of cleavage. J. Biol. Chem., 251, 3807-3814.
15. Kieft,J.S., Zhou,K., Jubin,R., Murray,M.G., Lau,J.Y. and Doudna,J.A. (1999) The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold. J. Mol. Biol., 292, 513-529.
16. Lyons,A.J., Lytle,J.R., Gomez,J. and Robertson,H.D. (2001) Hepatitis C virus internal ribosome entry site RNA contains a tertiary structural element in a functional domain of stem-loop II. Nucleic Acids Res., 29, 2535-2541.
17. Henke,J.I., Goergen,D., Zheng,J., Song,Y., Schuttler,C.G., Fehr,C., Junemann,C. and Niepmann,M. (2008) microRNA-122 stimulates translation of hepatitis C virus RNA. EMBO J., 27, 3300-3310.
18. Huthoff,H. and Berkhout,B. (2001) Two alternating structures of the HIV-1 leader RNA. RNA, 7, 143-157.
19. Jopling,C.L., Schutz,S. and Sarnow,P. (2008) Position-dependent function for a tandem microRNA miR-122-binding site located in the hepatitis C virus RNA genome. Cell Host Microbe., 4, 77-85.
20. Sarasin-Filipowicz,M., Krol,J., Markiewicz,I., Heim,M.H. and Filipowicz,W. (2009) Decreased levels of microRNA miR-122 in individuals with hepatitis C responding poorly to interferon therapy. Nat. Med., 15, 31-33.
21. Agnello,V., Abel,G., Knight,G.B. and Muchmore,E. (1998) Detection of widespread hepatocyte infection in chronic hepatitis C. Hepatology, 28, 573-584.